[BioC] Normalization quality

alex lam (RI) alex.lam at bbsrc.ac.uk
Thu Oct 5 12:22:33 CEST 2006

Dear BioCers,

Hi! I don't have much of experience in handling affy chips and I hope
someone can help me here.

I loaded 276 affy CEL files using justGCRMA - my computer couldn't cope
going the readAffy route.
Quantile normalization was done.

I have noticed that for some probesets there are some strange results.
For example:
> summary(exprs(eset.norm.quantile)["203329_at",])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
  2.486   2.513   2.523   2.545   2.534   5.201

This gene seems to be very lowly expressed for everyone except for 1
chip. I did a boxplot of that chip against a few others after
normalization and the overall distributions are similar.

(1) As I don't have an AffyBatch object, is there a way to make image
plots? And what other methods are there to catch these odd ones?       

(2) I was provided summarised expression values from an external group
and they used MAS5 for pre-processing. For the same gene, the expression
summary is:
> summary(mas.expr[,"X203329_at"]) # I received a csv file, hence it's a
data frame
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.926   5.337   5.950   5.880   6.403   9.183
The variation seems to be much greater, and it looks much more
interesting. Can I expect such difference? Is it just because of gcrma
works in the natural log scale or is there something wrong with my

Many thanks for your help.
Best wishes,

Alex Lam
PhD student
Department of Genetics and Genomics
Roslin Institute (Edinburgh)
Midlothian EH25 9PS

Phone +44 131 5274471
Web   http://www.roslin.ac.uk

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